Contacts of the helix formed by residues 605 - 612 (chain A) in PDB entry 3I5H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 605 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A CYS 5.7 1.1 - - - +
401A LEU* 6.0 1.2 - - - +
417A ARG* 5.8 1.4 + - - -
425A SER* 3.7 42.9 + - - +
428A ALA* 4.8 0.8 - - - +
429A LEU* 5.6 1.6 - - - +
603A PRO* 4.0 14.1 + - - +
604A ILE* 1.3 80.5 - - - +
606A GLU* 1.3 51.0 + - - +
607A ASN* 2.7 6.2 + - - +
608A VAL* 2.4 57.6 + - + +
609A VAL* 4.6 1.5 - - - +
644A PHE* 3.9 18.6 - - - -
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Residues in contact with GLU 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A ILE* 5.1 19.2 - - + +
604A ILE* 3.6 14.4 + - + +
605A ASN* 1.3 69.6 - - - +
607A ASN* 1.3 61.0 + - - +
609A VAL* 2.5 44.9 + - - +
610A GLU* 3.3 9.2 + - + +
643A ALA* 5.9 2.8 - - - +
644A PHE* 5.0 14.0 - - + -
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Residues in contact with ASN 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A CYS* 4.3 14.6 - - + +
404A PRO* 3.1 36.9 - - + +
405A LYS 3.2 19.3 - - - +
406A ILE* 3.8 25.2 - - - +
605A ASN* 2.7 7.0 + - - +
606A GLU* 1.3 77.8 - - - +
608A VAL* 1.3 57.6 + - + +
610A GLU* 4.1 6.6 - - - +
611A LEU* 2.9 34.2 + - - +
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Residues in contact with VAL 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A LEU* 4.7 8.3 - - + -
400A CYS* 4.5 13.9 - - + +
401A LEU* 4.2 27.6 - - + -
429A LEU* 4.2 17.0 - - + -
605A ASN* 2.4 50.6 + - + +
607A ASN* 1.3 73.8 - - + +
609A VAL* 1.3 48.3 + - + +
611A LEU* 3.8 6.2 - - + +
612A LEU* 2.7 66.0 + - + +
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Residues in contact with VAL 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A ARG* 4.7 17.3 - - - +
604A ILE* 4.3 16.6 - - + -
605A ASN 4.8 0.9 - - - +
606A GLU* 2.5 35.2 + - - +
608A VAL* 1.3 65.3 - - + +
610A GLU* 1.3 60.7 + - + +
612A LEU* 2.5 30.6 + - - +
613A GLN* 2.8 36.3 + - - +
623A LEU* 4.0 18.1 - - + +
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Residues in contact with GLU 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A GLU* 4.2 12.1 - - + +
607A ASN* 4.1 7.6 - - - +
609A VAL* 1.3 80.9 - - + +
611A LEU* 1.3 59.1 + - - +
613A GLN* 2.7 68.0 + - - +
614A ASN* 4.1 4.2 + - - +
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Residues in contact with LEU 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A VAL* 3.6 30.4 - - + +
396A ASP* 4.1 17.0 - - + +
397A LEU* 3.7 23.6 - - + +
400A CYS* 3.1 34.5 - - + -
607A ASN 2.9 20.0 + - - +
608A VAL* 3.8 5.4 - - + +
610A GLU* 1.3 76.2 - - - +
612A LEU* 1.3 59.1 + - + +
613A GLN 3.0 4.9 + - - -
614A ASN* 3.1 29.8 + - - +
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Residues in contact with LEU 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU* 3.7 31.2 - - + -
392A VAL* 4.4 15.5 - - + -
397A LEU* 5.9 3.8 - - + -
429A LEU* 3.4 23.3 - - + -
608A VAL* 2.7 47.0 + - + +
609A VAL* 2.5 15.7 + - - +
611A LEU* 1.3 73.6 - - + +
613A GLN* 1.3 55.2 + - - +
614A ASN 3.3 6.5 + - - -
619A ILE* 3.7 12.1 - - + +
623A LEU* 3.2 50.4 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il